Have you tried just loading the sequence into memory using
Bio::SeqIO? The problem may be the size of the file itself.
chris
On Jul 3, 2008, at 6:48 AM, Andreas Dräger wrote:
> Hi all,
>> Recently I have successfully installed the latest version of BioPerl
> and BioSQL on my computer, which has 2 GB RAM. Both works fine, but
> when trying to insert the genbank file of the human chromosome 1,
> which I have downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/CHR_01/hs_ref_chr1.gbk.gz> ) I receive the error message 'Out of memory'. This takes about one
> hour. My question is, how I can insert large genbank files in my
> BioSQL database using BioPerl. I do not know, what to do. Thank you
> for your help!!!
>> Cheers,
> Andreas
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign